{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,25]],"date-time":"2026-09-25T16:34:09Z","timestamp":1790354049362,"version":"4.1.0"},"reference-count":41,"publisher":"American Society for Microbiology","issue":"8","license":[{"start":{"date-parts":[[2025,8,5]],"date-time":"2025-08-05T00:00:00Z","timestamp":1754352000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["Microbiol Spectr"],"published-print":{"date-parts":[[2025,8,5]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:sec>\n                    <jats:title\/>\n                    <jats:p>\n                      Echinocandins are the recommended antifungal therapy for\n                      <jats:italic toggle=\"yes\">Candida auris<\/jats:italic>\n                      infections in many countries. While echinocandin resistance remains uncommon, recent reports demonstrate an increase in such cases, with the potential for echinocandin-resistant\n                      <jats:italic toggle=\"yes\">C. auris<\/jats:italic>\n                      transmission between persons. The expansion of\n                      <jats:italic toggle=\"yes\">C. auris<\/jats:italic>\n                      whole-genome sequencing capacity in public health laboratories provides a great opportunity to leverage genomic data to detect echinocandin resistance-conferring mutations. However, curated datasets for validating genomic tools for these purposes are lacking. Therefore, we developed a benchmark dataset comprising 100 whole-genome sequenced\n                      <jats:italic toggle=\"yes\">C. auris<\/jats:italic>\n                      isolates categorized as echinocandin-susceptible (\n                      <jats:italic toggle=\"yes\">n<\/jats:italic>\n                      = 53) and resistant (\n                      <jats:italic toggle=\"yes\">n<\/jats:italic>\n                      = 47) by antifungal susceptibility testing. We implemented the fungal bioinformatics pipeline, MycoSNP-nf, to perform whole-genome sequencing analysis, including\n                      <jats:italic toggle=\"yes\">C. auris<\/jats:italic>\n                      clade typing and the detection of\n                      <jats:italic toggle=\"yes\">FKS1<\/jats:italic>\n                      mutations in hotspot (HS) regions. Phylogenetic analysis classified isolates into four major clades (Clades I\u2013IV). Of the 47 isolates considered resistant by AFST, 44 showed HS mutations identified by MycoSNP-nf\u2014with 41 positioned in two well-described HS regions and 3 within a potential third hotspot that was recently reported. This benchmark dataset is designed to be a resource to build sequencing capacity to detect echinocandin resistance-conferring mutations in\n                      <jats:italic toggle=\"yes\">FKS1<\/jats:italic>\n                      and to help standardize comparisons across other bioinformatics tools.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>IMPORTANCE<\/jats:title>\n                    <jats:p>\n                      Echinocandins are the recommended first-line treatment for invasive infections caused by\n                      <jats:italic toggle=\"yes\">Candida auri<\/jats:italic>\n                      s, a multi-drug-resistant yeast that has emerged in healthcare facilities globally. Increasing instances of echinocandin-resistant cases highlight the need for rapid detection and response. We developed a benchmark dataset comprising 100\n                      <jats:italic toggle=\"yes\">C. auris<\/jats:italic>\n                      echinocandin-resistant and -susceptible isolates to demonstrate the utility of the bioinformatics tool, MycoSNP-nf, for detecting echinocandin resistance-related\n                      <jats:italic toggle=\"yes\">FKS1<\/jats:italic>\n                      mutations and to assess their concordance with antifungal susceptibility testing results. This benchmark may help validate MycoSNP-nf and other bioinformatics tools aimed at detecting these mechanisms using whole-genome sequencing data.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.1128\/spectrum.03147-24","type":"journal-article","created":{"date-parts":[[2025,6,18]],"date-time":"2025-06-18T08:32:33Z","timestamp":1750235553000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":8,"title":["A benchmark dataset for validating\n                    <i>FKS1<\/i>\n                    mutations in\n                    <i>Candida auris<\/i>"],"prefix":"10.1128","volume":"13","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6243-7716","authenticated-orcid":true,"given":"Elizabeth","family":"Misas","sequence":"first","affiliation":[{"id":[{"id":"https:\/\/ror.org\/00qzjvm58","id-type":"ROR","asserted-by":"publisher"}],"name":"Mycotic Diseases Branch, Centers for Disease Control and Prevention","place":["Atlanta, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5598-6485","authenticated-orcid":true,"given":"Lindsay A.","family":"Parnell","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/00qzjvm58","id-type":"ROR","asserted-by":"publisher"}],"name":"Mycotic Diseases Branch, Centers for Disease Control and Prevention","place":["Atlanta, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Malavika","family":"Rajeev","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/00qzjvm58","id-type":"ROR","asserted-by":"publisher"}],"name":"Mycotic Diseases Branch, Centers for Disease Control and Prevention","place":["Atlanta, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Luisa F.","family":"L\u00f3pez","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/00qzjvm58","id-type":"ROR","asserted-by":"publisher"}],"name":"Mycotic Diseases Branch, Centers for Disease Control and Prevention","place":["Atlanta, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5577-4498","authenticated-orcid":true,"given":"Amanda Ribeiro dos","family":"Santos","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/00qzjvm58","id-type":"ROR","asserted-by":"publisher"}],"name":"Mycotic Diseases Branch, Centers for Disease Control and Prevention","place":["Atlanta, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zachary B.","family":"Mudge","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/00qzjvm58","id-type":"ROR","asserted-by":"publisher"}],"name":"Mycotic Diseases Branch, Centers for Disease Control and Prevention","place":["Atlanta, USA"]},{"name":"APHL-CDC Public Health Laboratory Fellow, Centers for Disease Control and Prevention","place":["Bethesda, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lalitha","family":"Gade","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/00qzjvm58","id-type":"ROR","asserted-by":"publisher"}],"name":"Mycotic Diseases Branch, Centers for Disease Control and Prevention","place":["Atlanta, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kaitlin","family":"Forsberg","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/00qzjvm58","id-type":"ROR","asserted-by":"publisher"}],"name":"Mycotic Diseases Branch, Centers for Disease Control and Prevention","place":["Atlanta, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Meghan","family":"Lyman","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/00qzjvm58","id-type":"ROR","asserted-by":"publisher"}],"name":"Mycotic Diseases Branch, Centers for Disease Control and Prevention","place":["Atlanta, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3099-7334","authenticated-orcid":true,"given":"D. Joseph","family":"Sexton","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/00qzjvm58","id-type":"ROR","asserted-by":"publisher"}],"name":"Mycotic Diseases Branch, Centers for Disease Control and Prevention","place":["Atlanta, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1086-8041","authenticated-orcid":true,"given":"Anastasia P.","family":"Litvintseva","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/00qzjvm58","id-type":"ROR","asserted-by":"publisher"}],"name":"Mycotic Diseases Branch, Centers for Disease Control and Prevention","place":["Atlanta, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4383-5994","authenticated-orcid":true,"given":"Shawn R.","family":"Lockhart","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/00qzjvm58","id-type":"ROR","asserted-by":"publisher"}],"name":"Mycotic Diseases Branch, Centers for Disease Control and Prevention","place":["Atlanta, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nancy A.","family":"Chow","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/00qzjvm58","id-type":"ROR","asserted-by":"publisher"}],"name":"Mycotic Diseases Branch, Centers for Disease Control and Prevention","place":["Atlanta, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_4_2_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1348-0421.2008.00083.x"},{"key":"e_1_3_4_3_2","unstructured":"World Health Organization. 2022. 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